The cells that constitute different tissues in an organism, although having the same genomic DNA, differ significantly from one another with respect to the specific genes that are expressed and the levels of expression. Similar differences in gene expression can be observed when comparing cells that are obtained from a healthy organism and corresponding cells from an organism manifesting a disease state. Other examples of variations in gene expression include changes induced by exposing a cell to a pharmaceutical compound or toxin. It is of interest to provide methods for analyzing changes in gene expression. Methods of analyzing gene expression find wide use in both research and diagnostics.